Variant report

Variant	rs10945242
Chromosome Location	chr6:71426558-71426559
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10498874	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs10498875	0.86[YRI][hapmap]
rs10755541	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs10755543	0.86[YRI][hapmap]
rs1084388	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs11962454	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12190398	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12201672	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202843	0.86[YRI][hapmap]
rs12203717	0.89[JPT][hapmap]
rs12209357	0.86[YRI][hapmap]
rs12209431	0.85[YRI][hapmap]
rs12210698	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12212629	0.86[YRI][hapmap]
rs12215757	0.80[LWK][hapmap];0.85[YRI][hapmap]
rs12215835	0.86[YRI][hapmap]
rs1333965	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16880774	0.89[JPT][hapmap]
rs2347433	0.86[YRI][hapmap]
rs2474913	0.86[YRI][hapmap]
rs4706461	0.82[YRI][hapmap]
rs4706463	0.86[YRI][hapmap]
rs4707851	0.86[YRI][hapmap]
rs55733349	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62419707	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62419724	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62419729	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62419736	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62419740	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs781964	0.86[YRI][hapmap]
rs781967	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs781968	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs781971	0.88[YRI][hapmap]
rs781977	0.86[YRI][hapmap]
rs781978	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs781982	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs781983	0.80[LWK][hapmap];0.82[YRI][hapmap]
rs781989	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs781992	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10945242	SMAP1	cis	multi-tissue	Pritchard
rs10945242	OGFRL1	cis	cerebellum	SCAN
rs10945242	SMAP1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71418200-71426800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:71420000-71435200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:71420000-71436800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:71422000-71435200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:71423000-71426600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:71425400-71426800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:71425400-71427000	Weak transcription	Aorta	Aorta
8	chr6:71425400-71427000	Weak transcription	Thymus	Thymus
9	chr6:71425400-71442600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:71425800-71426600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:71425800-71427800	Enhancers	GM12878-XiMat	blood
12	chr6:71426000-71427200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:71426000-71427200	Enhancers	Gastric	stomach
14	chr6:71426000-71427200	Enhancers	Pancreas	Pancrea
15	chr6:71426000-71427200	Enhancers	Psoas Muscle	Psoas
16	chr6:71426000-71427400	Enhancers	Right Atrium	heart
17	chr6:71426000-71427600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:71426000-71428200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:71426000-71428200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:71426200-71426600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:71426200-71427000	Weak transcription	Left Ventricle	heart
22	chr6:71426200-71428400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:71426200-71428400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:71426200-71443800	Weak transcription	Lung	lung
25	chr6:71426200-71451000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:71426400-71427200	Enhancers	Adipose Nuclei	Adipose
27	chr6:71426400-71427400	Enhancers	Fetal Heart	heart
28	chr6:71426400-71428200	Enhancers	Primary T cells from cord blood	blood
29	chr6:71426400-71428200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr6:71426400-71443000	Weak transcription	Primary B cells from cord blood	blood

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